Mover that computes which residues are lipid accessible and puts that information into the B-factors: 50 is lipid accessible, 0 is lipid INaccessible. More...
#include <MPLipidAccessibility.hh>
Public Member Functions | |
| MPLipidAccessibility () | |
| Constructors ///. More... | |
| ~MPLipidAccessibility () override | |
| Copy constructor (not needed unless you need deep copies) More... | |
| void | apply (core::pose::Pose &pose) override |
| Mover Methods ///. More... | |
| void | show (std::ostream &output=std::cout) const override |
| Show the contents of the Mover. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
| Get the name of the Mover. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| required in the context of the parser/scripting scheme More... | |
| protocols::moves::MoverOP | clone () const override |
| required in the context of the parser/scripting scheme More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| core::Real | get_angle_cutoff () const |
| Get Methods ///. More... | |
| core::Real | get_slice_width () const |
| get slice width More... | |
| void | set_slice_width (core::Real width) |
| @Brief Set slice width via commandline More... | |
| core::Real | get_shell_radius () const |
| get shell radius More... | |
| core::Real | get_dist_cutoff () const |
| get dist cutoff More... | |
| bool | get_tm_alpha () const |
| get tm_alpha More... | |
| bool | is_alpha_helical () const |
| Is this an alpha helical protein? (no >7 exception) More... | |
 Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual MoverOP | create () |
| MoverCOP | get_self_ptr () const |
| MoverOP | get_self_ptr () |
| MoverCAP | get_self_weak_ptr () const |
| MoverAP | get_self_weak_ptr () |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| virtual bool | reinitialize_for_each_job () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual bool | reinitialize_for_new_input () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
| MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | reset_status () |
| resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
| virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| void | set_type (std::string const &setting) |
| Set the 'type' string. More... | |
| std::string | get_type () const |
| void | type (const std::string &type_in) |
| Set the 'type' string. More... | |
| std::string const & | type () const |
| Get the set 'type' string. More... | |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| virtual void | clear_info () |
| Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
| virtual Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
| static std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| Overload this static method if you access options within the mover. More... | |
Private Member Functions | |
| void | set_defaults () |
| set defaults More... | |
| void | register_options () |
| Register Options from Command Line. More... | |
| void | init_from_cmd () |
| Initialize from commandline. More... | |
| void | finalize_setup (Pose &pose) |
| finalize setup More... | |
| bool | protein_in_membrane (Pose &pose) |
| check whether protein is in membrane More... | |
| void | fill_up_slices (Pose &pose) |
| fill up slice arrays with protein data More... | |
| void | compute_slice_com () |
| compute slice COM More... | |
Private Attributes | |
| core::Real | angle_cutoff_ |
| original data from first implementation More... | |
| core::Real | slice_width_ |
| core::Real | shell_radius_ |
| core::Real | dist_cutoff_ |
| bool | tm_alpha_ |
| bool | is_alpha_helical_ |
| utility::vector1< utility::vector1< core::Size > > | resi_ |
| utility::vector1< utility::vector1< core::Vector > > | ca_coord_ |
| utility::vector1< utility::vector1< core::Vector > > | cb_coord_ |
| utility::vector1< core::Vector > | slice_com_ |
| utility::vector1< core::Real > | slice_zmin_ |
| utility::vector1< utility::vector1< core::Real > > | per_atom_lipid_accessibility_ |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef std::list< std::string > | Strings |
| Protected Member Functions inherited from protocols::moves::Mover | |
| void | set_last_move_status (MoverStatus status) |
| nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Detailed Description
Mover that computes which residues are lipid accessible and puts that information into the B-factors: 50 is lipid accessible, 0 is lipid INaccessible.
Constructor & Destructor Documentation
◆ MPLipidAccessibility()
| protocols::membrane::MPLipidAccessibility::MPLipidAccessibility | ( | ) |
Constructors ///.
Default constructor
References init_from_cmd(), register_options(), and set_defaults().
◆ ~MPLipidAccessibility()
|
overridedefault |
Copy constructor (not needed unless you need deep copies)
Destructor (important for properly forward-declaring smart-pointer members)
Member Function Documentation
◆ apply()
|
overridevirtual |
Mover Methods ///.
MOVER METHODS ///.
Apply the mover
Implements protocols::moves::Mover.
References core::pose::motif::a(), angle_cutoff_, ca_coord_, cb_coord_, core::membrane::concave_shell(), core::pose::Pose::conformation(), dist_cutoff_, finalize_setup(), core::id::AtomID_Map< T >::get(), core::id::AtomID_Map< T >::has(), core::conformation::Conformation::membrane_info(), core::pose::Pose::membrane_info(), core::conformation::Residue::natoms(), core::pose::nres_protein(), core::pose::Pose::pdb_info(), resi_, core::pose::Pose::residue(), shell_radius_, slice_com_, slice_width_, slice_zmin_, tm_alpha_, and protocols::TR().
◆ clone()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ compute_slice_com()
|
private |
compute slice COM
References ca_coord_, protocols::membrane::com(), resi_, slice_com_, slice_zmin_, and protocols::TR().
Referenced by fill_up_slices().
◆ fill_up_slices()
|
private |
fill up slice arrays with protein data
References ca_coord_, cb_coord_, compute_slice_com(), core::pose::Pose::conformation(), core::conformation::Conformation::is_membrane(), core::pose::Pose::membrane_info(), core::conformation::Residue::name3(), core::pose::nres_protein(), resi_, core::pose::Pose::residue(), slice_width_, slice_zmin_, core::conformation::membrane::thickness, and core::conformation::Residue::xyz().
Referenced by finalize_setup().
◆ finalize_setup()
|
private |
finalize setup
References angle_cutoff_, core::pose::Pose::conformation(), fill_up_slices(), protocols::membrane::get_secstruct(), is_alpha_helical_, core::pose::Pose::membrane_info(), core::pose::nres_protein(), protein_in_membrane(), tm_alpha_, and protocols::TR().
Referenced by apply().
◆ fresh_instance()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ get_angle_cutoff()
| core::Real protocols::membrane::MPLipidAccessibility::get_angle_cutoff | ( | ) | const |
◆ get_dist_cutoff()
| core::Real protocols::membrane::MPLipidAccessibility::get_dist_cutoff | ( | ) | const |
get dist cutoff
References dist_cutoff_.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ get_shell_radius()
| core::Real protocols::membrane::MPLipidAccessibility::get_shell_radius | ( | ) | const |
get shell radius
References shell_radius_.
◆ get_slice_width()
| core::Real protocols::membrane::MPLipidAccessibility::get_slice_width | ( | ) | const |
get slice width
References slice_width_.
◆ get_tm_alpha()
| bool protocols::membrane::MPLipidAccessibility::get_tm_alpha | ( | ) | const |
get tm_alpha
References tm_alpha_.
◆ init_from_cmd()
|
private |
Initialize from commandline.
References angle_cutoff_, dist_cutoff_, shell_radius_, slice_width_, and tm_alpha_.
Referenced by MPLipidAccessibility().
◆ is_alpha_helical()
| bool protocols::membrane::MPLipidAccessibility::is_alpha_helical | ( | ) | const |
Is this an alpha helical protein? (no >7 exception)
References is_alpha_helical_.
◆ mover_name()
|
static |
Referenced by get_name(), protocols::membrane::MPLipidAccessibilityCreator::keyname(), and provide_xml_schema().
◆ parse_my_tag()
|
overridevirtual |
Get the name of the Mover.
Rosetta Scripts Support ///.
Rosetta Scripts Support ///
parse XML tag (to use this Mover in Rosetta Scripts)
parse XML tag (to use this Mover in Rosetta Scripts)
Reimplemented from protocols::moves::Mover.
References angle_cutoff_, dist_cutoff_, shell_radius_, slice_width_, and tm_alpha_.
◆ protein_in_membrane()
|
private |
check whether protein is in membrane
check whether protein is transformed into membrane
References core::conformation::Residue::name3(), core::pose::nres_protein(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().
Referenced by finalize_setup().
◆ provide_xml_schema()
|
static |
References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::membrane::MPLipidAccessibilityCreator::provide_xml_schema().
◆ register_options()
|
private |
Register Options from Command Line.
Referenced by MPLipidAccessibility().
◆ set_defaults()
|
private |
set defaults
private methods ///
set defaults
References angle_cutoff_, dist_cutoff_, is_alpha_helical_, shell_radius_, slice_width_, and tm_alpha_.
Referenced by MPLipidAccessibility().
◆ set_slice_width()
| void protocols::membrane::MPLipidAccessibility::set_slice_width | ( | core::Real | width | ) |
@Brief Set slice width via commandline
set slice width (should be an integer multiple of membrane thickness)
References slice_width_.
◆ show()
|
overridevirtual |
Show the contents of the Mover.
Reimplemented from protocols::moves::Mover.
References protocols::moves::Mover::show().
Member Data Documentation
◆ angle_cutoff_
|
private |
original data from first implementation
Referenced by apply(), finalize_setup(), get_angle_cutoff(), init_from_cmd(), parse_my_tag(), and set_defaults().
◆ ca_coord_
|
private |
Referenced by apply(), compute_slice_com(), and fill_up_slices().
◆ cb_coord_
|
private |
Referenced by apply(), and fill_up_slices().
◆ dist_cutoff_
|
private |
Referenced by apply(), get_dist_cutoff(), init_from_cmd(), parse_my_tag(), and set_defaults().
◆ is_alpha_helical_
|
private |
Referenced by finalize_setup(), is_alpha_helical(), and set_defaults().
◆ per_atom_lipid_accessibility_
|
private |
◆ resi_
|
private |
Referenced by apply(), compute_slice_com(), and fill_up_slices().
◆ shell_radius_
|
private |
Referenced by apply(), get_shell_radius(), init_from_cmd(), parse_my_tag(), and set_defaults().
◆ slice_com_
|
private |
Referenced by apply(), and compute_slice_com().
◆ slice_width_
|
private |
Referenced by apply(), fill_up_slices(), get_slice_width(), init_from_cmd(), parse_my_tag(), set_defaults(), and set_slice_width().
◆ slice_zmin_
|
private |
Referenced by apply(), compute_slice_com(), and fill_up_slices().
◆ tm_alpha_
|
private |
Referenced by apply(), finalize_setup(), get_tm_alpha(), init_from_cmd(), parse_my_tag(), and set_defaults().
The documentation for this class was generated from the following files:
- src/protocols/membrane/MPLipidAccessibility.hh
- src/protocols/membrane/MPLipidAccessibility.cc
